Contacts of the strand formed by residues 2118 - 2123 (chain B) in PDB entry 2DQZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR2118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B SIA 4.3 18.9 + - - -
2052B GLY* 3.2 30.7 - - - -
2053B ILE 3.2 6.7 - - - +
2054B PRO* 3.6 26.5 - - + -
2055B PHE* 3.3 7.7 - - - -
2058B PRO* 5.2 0.7 - - - +
2084B PRO* 3.7 30.3 - - + -
2085B PRO* 4.3 9.4 - - + -
2115B ASP* 2.8 54.7 + - - -
2116B CYS* 2.6 22.8 + - - +
2117B LEU* 1.3 74.5 - - - +
2119B LEU* 1.3 61.7 + - - +
2169B GLN* 3.2 29.0 + - - +
3184C HIS* 4.9 8.5 + - - -
3278C THR* 4.7 4.7 - - + -
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Residues in contact with LEU2119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2052B GLY 3.6 0.5 + - - -
2053B ILE* 2.9 47.4 + - + +
2055B PHE* 3.8 29.4 - - + -
2084B PRO* 6.1 0.2 - - - -
2118B TYR* 1.3 76.3 - - - +
2120B ASN* 1.3 66.8 + - - +
2121B ILE* 3.7 33.2 - - + -
2149B ALA* 5.7 0.7 - - - -
2166B VAL* 4.2 8.7 - - + -
2167B THR 3.1 13.5 - - - +
2168B ILE* 4.0 13.0 - - + -
2197B ALA* 4.4 15.7 - - + +
2200B TRP* 4.0 22.4 - - + -
2201B VAL* 4.9 0.9 - - + -
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Residues in contact with ASN2120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2050B PHE 3.4 6.7 - - - +
2051B LEU* 3.4 15.9 - - + +
2052B GLY* 2.9 26.3 + - - -
2083B TYR* 4.5 0.8 - - - -
2084B PRO* 3.6 10.8 - - - +
2119B LEU* 1.3 76.2 - - - +
2121B ILE* 1.3 63.6 + - - +
2122B TYR* 3.9 16.6 + - + -
2149B ALA* 4.2 3.4 - - - +
2150B SER* 3.5 36.0 + - - +
2152B TYR 5.6 0.2 + - - -
2165B VAL 3.8 0.5 - - - +
2166B VAL* 3.3 4.9 - - - +
2167B THR* 2.7 51.5 + - - +
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Residues in contact with ILE2121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2048B ALA 3.7 0.7 - - - +
2049B ILE* 3.4 6.4 - - - +
2050B PHE* 2.9 43.3 + - + +
2053B ILE* 3.8 14.8 - - + -
2119B LEU* 3.7 15.9 - - + -
2120B ASN* 1.3 76.9 - - - +
2122B TYR* 1.3 77.6 + - - +
2123B THR* 4.1 3.6 - - + +
2164B VAL* 4.1 19.1 - - + -
2165B VAL 3.6 2.9 - - - +
2166B VAL* 4.1 10.1 - - + -
2200B TRP* 3.8 31.6 - - + -
2205B ILE* 4.2 7.4 - - + -
2208B PHE* 3.9 29.2 - - + -
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Residues in contact with TYR2122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2047B VAL* 4.4 3.4 - - + -
2048B ALA 3.6 4.0 - - - -
2049B ILE* 3.5 40.8 - - + -
2051B LEU* 3.8 15.7 - - + +
2083B TYR* 4.6 1.9 + - - -
2104B ARG* 4.0 18.5 + - - -
2120B ASN* 3.9 26.7 + - + +
2121B ILE* 1.3 78.3 - - - +
2123B THR* 1.3 61.2 + - - +
2124B PRO* 4.2 0.4 - - - -
2150B SER* 5.7 0.2 - - - -
2152B TYR 4.0 6.7 + - - -
2153B ASP* 3.3 16.2 - - - -
2154B GLY* 3.8 20.4 - - - -
2155B LEU* 3.7 13.9 - - - -
2158B ALA* 3.8 20.8 - - + +
2164B VAL* 3.4 2.4 - - - -
2165B VAL* 2.8 49.8 + - + +
2167B THR* 4.5 6.7 - - + -
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Residues in contact with THR2123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2046B PRO 4.8 0.2 - - - +
2047B VAL* 3.8 2.9 - - - +
2048B ALA* 2.8 54.5 + - + +
2050B PHE* 4.4 6.7 - - + -
2121B ILE* 4.6 1.6 - - + -
2122B TYR* 1.3 74.5 - - - +
2124B PRO* 1.3 60.8 - - - +
2125B ALA* 3.2 17.9 + - - +
2127B LEU* 4.3 12.3 - - + -
2164B VAL* 3.7 16.4 - - - +
2208B PHE* 2.6 37.9 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il